Solubility parameter based methods have long been a valuable tool for solvent formulation and selection. Of these methods, the MOdified Separation of Cohesive Energy Density (MOSCED) has recently been shown to correlate well the equilibrium solubility of multifunctional non-electrolyte solids. However, before it can be applied to a novel solute, a limited amount of reference solubility data is required to regress the necessary MOSCED parameters. Here we demonstrate for the solutes methylparaben, ethylparaben, propylparaben, butylparaben, lidocaine and ephedrine how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here the SMD or SM8 solvation model, can instead be used to generate the necessary reference data, resulting in a predictive flavor of MOSCED. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. We find the method is able to well correlate the (mole fraction) equilibrium solubility in non-aqueous solvents over four orders of magnitude with good quantitative agreement.
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http://dx.doi.org/10.1007/s10822-016-0001-6 | DOI Listing |
PLoS One
December 2024
Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon, Republic of Korea.
The increasing utilization of deep learning models in drug repositioning has proven to be highly efficient and effective. In this study, we employed an integrated deep-learning model followed by traditional drug screening approach to screen a library of FDA-approved drugs, aiming to identify novel inhibitors targeting the TNF-α converting enzyme (TACE). TACE, also known as ADAM17, plays a crucial role in the inflammatory response by converting pro-TNF-α to its active soluble form and cleaving other inflammatory mediators, making it a promising target for therapeutic intervention in diseases such as rheumatoid arthritis.
View Article and Find Full Text PDFJ Chem Theory Comput
December 2024
School of Pharmaceutical Sciences and Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Rue Michel Servet 1, 1206 Genève, Switzerland.
We introduce an enhanced sampling algorithm to obtain converged free energy landscapes of molecular rare events, even when the collective variable (CV) used for biasing is not optimal. Our approach samples a time-dependent target distribution by combining the on-the-fly probability enhanced sampling and its exploratory variant, OPES Explore. This promotes more transitions between the relevant metastable states and accelerates the convergence speed of the free energy estimate.
View Article and Find Full Text PDFSynapse
January 2025
Department of Biochemistry & Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh.
Sesamol (SES) and linalool (LIN) are aromatic compounds that have neuroprotective effects. The main purpose of this study is to evaluate the anxiolytic activity of LIN and SES co-treatment on Swiss albino mice and analyze its possible mechanism through in silico study. In this sense, the mice were given the gamma-aminobutyric acid type A receptors (GABA) agonist diazepam (DZP; 3 mg/kg, p.
View Article and Find Full Text PDFJ Phys Chem A
December 2024
State Key Laboratory of Mesoscience and Engineering, Institute of Process Engineering, Chinese Academy of Science s, Beijing 100190, China.
To understand the mechanism of self-assembly and to predict the evolutionary pattern of the fusion-fission system over a long period of time, studying the dynamics of these processes is of great significance. The trajectories from molecular dynamics (MD) simulations of self-assembly processes contain numerous latent fusion and fission events. To analyze the fusion and fission events from the simulated trajectory, in this article, a dynamic clustering approach was developed by comparing the changes of monomer composition within clusters over simulated time.
View Article and Find Full Text PDFNanomaterials (Basel)
December 2024
Guangdong Provincial Key Laboratory of Photonics Information Technology, Guangdong University of Technology, Guangzhou 510006, China.
The in situ and label-free detection of molecular information in biological cells has always been a challenging problem due to the weak Raman signal of biological molecules. The use of various resonance nanostructures has significantly advanced Surface-enhanced Raman spectroscopy (SERS) in signal enhancement in recent years. However, biological cells are often immersed in different formulations of culture medium with varying refractive indexes and are highly sensitive to the temperature of the microenvironment.
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